Afterwards
by hr-gw
Summary: This story is my vision of what should happen after the season 3 finale. It will not contain the scenes from Season 4 but I may use some of the facts there. Enjoy!
1. Chapter 1

I love Prison Break very much. I really don't understand how the writers can be that creative. I have been working on this story for a while (in fact, I first came up with the idea after the season 3 finale) and at last find the courage to upload it. And I would like to share it with you. Comments are welcome!

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**CHAPTER ONE**

It was a rainy day. In fact, the rain was fairly heavy. There were not many people on the street in Panama City. Most people had been home under this ridiculous weather, except a few homeless men. They would just sit under the roof, taking cover of the heavy rain.

LJ dashed across the street. He didn't bring an umbrella when he went out this afternoon. "No boys would take umbrella," LJ told Sophia. And he seriously regretted that. Indeed, all his clothes were soaking wet. He asked himself why bothered to run back home anyway. But then, he thought Sophia and his dad would definitely shout at him to see him like this. Trying to run back home may at least show he tried his best not to catch a cold.

LJ continued to run on this now almost empty street. The street lights were on but the homeless people looked more like the ghosts rather than the human beings. Some of them were shivering, as LJ could tell. In the past, LJ would try to talk to these people, asking how they were holding up. He had a knack of knowing everything and everyone. He was one of the typical curious teenagers. But after what he'd been through in the past few months, he would like to keep a low profile and not to gain attention anymore.

LJ passed from one building to another building. He ran very fast as the rain got heavier. After some time, he stopped under the roof of the bread shop to catch his breath. When he was trying to even his breath, he caught a glimpse of a man sitting in the corner. LJ could only see his back. But the odd posture of the man was already enough to make LJ change from looking to observing. LJ noted that the man wore a hooded jacket and the rain poured over him like waterfall. He was soaking wet because there was no way the little lamp post next to him could provide him any shelter from the rain. But none of it seemed to bother him. The man was sitting so still that LJ couldn't even tell whether he was alive.

"This man must be crazy," LJ reasoned. Every instinct told him that he should just leave the man alone. One of the first things he learnt when he attended high school was not to look for troubles. However, LJ couldn't push away the what-if questions. What if he needed help right now? What if he died because I ignored him now? I couldn't just run home like this, could I?

LJ was a good kid. He walked towards him, feeling the pounding of his heart as he got closer. The man didn't even flinch. Finally, LJ was just a few feet behind him. He was smart enough to keep certain distance and asked, "Hey, are you okay?" The man stirred and slowly turned himself towards LJ. "What if he was the company?" LJ suddenly thought and he was afraid.

It was too late to take it back anyway. The man raised his head and … both of them were stunned when their eyes met. "Uncle Mike?" LJ uttered softly, still couldn't believe who he had just seen.

"LJ? Why are you here?" Michael was actually as surprised as LJ when he saw him. But he recovered quickly. He told LJ, "LJ, promise me that you won't tell Linc. Just forget that you've seen me here, okay?" Michael then stood up and walked away.

LJ was surprised at seeing Michael here. After Mike saved him from Gretchen (yes, the horrible bitch), he just disappeared out of the hospital. Linc didn't tell him where Michael had gone, just saying that he needed to take care of something before he could live with them again. LJ assumed Michael would call before he came back. It didn't matter because LJ always liked surprise. But the fact that Michael said good–bye without even speaking to his dad was a shock. And LJ didn't really like that much.

LJ ran after Michael. "Wait, Uncle Mike. Where are you going? Why don't you come with me? Dad must love to see you," LJ said.

"No, he wouldn't," Michael replied and he didn't stop walking.

"Why would you say so?" LJ was totally confused.

"Look, just pretend that you have never seen me."

"And you think I can do that?"

"You have to. It's for your own good."

"Dad said that you would come live with us after you've taken care of things. Have you finished that?"

Michael stopped and he didn't know what to say. Did LJ need to know what he had done?

LJ sensed that something was not right. He thought he may have said something wrong. "Uncle Mike?" he said after a while when Michael was in front of him thinking about whatever there was in his mind.

Michael looked at LJ and said, "Go home, LJ. Be a good man. I love you." Then, he walked away.

"Uncle Mike, hold up," LJ tried to catch up with Michael but Michael pushed him away. "I mean what I said. Do not follow me!" Michael shouted and he kept on walking without looking back.

LJ didn't know what to do. He watched as Michael disappeared down the alley. The sadness he was feeling was a stabbing pain.

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I just hope that I haven't bored you to death! I know there's so much I need to improve and I promise I'll try. Next chapter will be about the brothers. I write that because I want to see more things about them on TV in which unfortunately this was nowhere to be found. So I figured I may as well use my imagination to satisfy myself. :)


	2. Chapter 2

**CHAPTER TWO**

"Dad, I'm home," LJ said as he entered the door. Linc looked up from the newspaper and said angrily, "Told you to bring an umbrella. See how wet you are!" "Guess he needs a change of clothes," Sophia said when she entered from the kitchen. She was always good to LJ. Unlike Lincoln, she was more understanding and kind. It was only a little more than a week since LJ and Sophia first met. But LJ began to like this woman. He even hoped that she could be his mother one day.

LJ gave Lincoln several glances when he wondered whether he should tell his father about Michael. Lincoln could sense his glances. LJ quickly looked away and began to go back to his room. Lincoln asked, "What happened?" "Well … nothing," LJ lied. "I look at you and I knew something happened. What is it?" Linc asked again. Lincoln was not a perfect dad but he knew his son after all. Are all fathers like that? LJ wondered. Do they all pretend that they don't notice anything even though they actually know everything?

Lincoln got up from the sofa and looked at his son straight in the eyes. "You know you're a lousy liar, son," Lincoln said. LJ didn't want to lie to his father, but he didn't want to betray his uncle too. So, he tried his best not to lie and not to tell the truth at the same time. "Well, something did happen. But it's okay now," he replied, hoping that Lincoln would drop the matter. He pretended that everything was cool and began to walk towards his bedroom once again.

LJ knew there would be 99% chance that Lincoln would push him to tell him exactly what happened. Could he blame his father for being so nosy? Because of what they had been through, the Fox River incident, the conspiracy and the kidnapping in Panama, Linc became much more alert to the events happening around him. "Sometimes, you just can't be too careful," he would say.

"So, what happened then?" Lincoln persisted as predicted. To be honest, he was worried about what LJ might tell him. It was not long when they finally settled down. The truth was it was actually a week. He just wanted to be normal. He wanted no business with the company anymore. It was so tiring to have to look over the shoulders all the time. All he wanted was to have a quiet life with the ones he loved. That was all he cared about.

LJ understood that his uncle Mike always made the right decision, the best decision for him and Lincoln anyway. He knew that his uncle told him not to tell Lincoln about their encounter for a reason. The reason might be just beyond his ability to understand. That was why he didn't tell him. "But it wouldn't hurt to tell Dad that you're alive, right? He's worried you sick!" LJ thought, recalling how many times Lincoln checked his cell phone every day.

"I saw Uncle Mike," LJ said finally.

"Michael? You saw Michael?" Lincoln suddenly became really nervous and continued, "Is he okay?"

"He looks fine."

"Where is he?"

"I don't know."

"What? What do you mean that you don't know?"

"He just left and told me not to tell you."

"And … and you just let him walk away?"

"I … I thought …" LJ suddenly felt he might have done something wrong to listen to his uncle.

"Don't tell me just watch him go away!" Lincoln said. When he saw the innocent expression on his son's face, he couldn't help but shouted, "Damn stupid!"

Sophia heard enough of their arguments. She came in and tried to soothe Lincoln. "Calm down, Linc. You're scary," she said softly.

"How the hell can I calm down? Michael is here. And he just tells my son not to tell me about this!" Lincoln said angrily.

"It's not like that," Sophia stated, "I guess he has a plan. Remember you tell me that he always has a plan. Don't worry about Michael. I think he'll show up when the time is right."

Lincoln took a deep breath and continued, "Why is it not the right time? Is the company going after him? Is he hurt? Does he need help? I've only got one brother, Sophia. I cannot stop worrying about him. You don't know Michael. He cares too much about others and so very often he … he …" Lincoln couldn't continue as he thought about how he ended up here instead of the electric chair in Fox River.

"He doesn't care about himself," LJ finished the sentence for his dad. "I'm sorry, dad. I was really stupid. I thought he had … I didn't … I didn't know he was pushing me away." LJ now understood why Michael asked him to go away. Michael was afraid that they might get hurt. And if Lincoln and LJ might get hurt by being with Michael, then Michael was in trouble.

"I wasn't there for him," Lincoln sighed heavily. Sophia put her hands on his shoulders, giving him some comfort. LJ looked at his father but all he could think of was his uncle who was soaking wet wandering on the street; facing the dangers all by himself.


	3. Chapter 3

**CHAPTER THREE**

"I need to go and find him," Lincoln announced in the living room. It was half an hour after LJ came home and told Linc that Michael was in Panama. During this half hour, LJ got a change of clothes and watched his father shout, yell and swear in whatever way he could. He knew how his father felt and thought it was really his mistake to let Michael go.

"What did I just do?" LJ thought, "Uncle Mike risked his life for me and I just let him walk away from me like that." Regretted as he was, he didn't know how he could fix this. He was angry. He was afraid. He was anxious. So when Lincoln said that he was going to find Michael, LJ immediately grabbed his backpack and decided to go too.

Sophia protested, "No, LJ. You stay." LJ said, "No way. I will help, Dad!"

Lincoln thought for a moment. "LJ, Sophia is right. I don't want you to come. Stay here and call me if Michael shows up. I'll be right back," Linc said and began to walk towards the door. LJ followed his father.

Linc noticed that LJ was behind him. He looked at LJ and said, "It's dangerous, LJ. Mike is still a wanted man in Panama and if a cop sees him, we've got to run. I'll do whatever I can to help Michael. Even if it means …"

"And so we'll do whatever we can to help Uncle Mike," LJ answered without even hearing the last part of Lincoln's sentence. Perhaps it was the urgency of the situation, or it was the determination Lincoln saw in his son's eyes, Linc nodded and went out. LJ followed closely behind.

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Linc and LJ were in their car which was moving pretty slowly. They needed to move around like this to make sure they could check every alley, every corner or perhaps every inch of the street. Panama City was not exactly a big place. The buildings were not tall. However, they were not built in a systematic way so that it was one of the best places for hide-and-seek, especially during the night. There was just no way for even the local people to tell where the beginning or the end of a street should be.

"You sure it's here?" Linc asked after checking the streets twice.

"Yes, this was where I saw Uncle Mike," LJ pointed at the lamp post and continued, "But dad, it was almost an hour ago. He must have gone."

Lincoln thought for a moment and said, "We should keep looking. I bet he's still here."

"Dad, you know. Maybe we should go to the nearby streets. I remember he was walking towards the Gardner Street the last time I saw him," LJ reasoned.

"You know what. We should get out of the car and check the area more closely. Michael is here. I know it," Lincoln said.

"How can you be so sure?"

"Because I'm his brother and your dad."

"Let me search the nearby neighbourhood, dad"

"We stay together, LJ."

"It'd be faster."

"It'd be dangerous."

"Look, the more we debate on this, the further away Uncle Mike may have gone!"

"You're right. So, get out of the damn car and follow me close!" Lincoln ended the conversation. LJ followed reluctantly. He loved his dad but still couldn't forgive his stubbornness sometimes.

Linc and LJ circled around the blocks carefully, looking everywhere they could. The rain had stopped, however it was still very difficult for them to search. Would Michael still be here? Lincoln questioned in his heart. Or would the company have already taken him out? Lincoln felt sick when he thought of this.

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They were close when they were small. And they knew each other well. Lincoln could always tell where Michael was. He could always understand what he was thinking and feeling. However, they grew apart when they got older. It was probably due to the different paths they had chosen. Lincoln was the rebellious son who always got himself into troubles. Michael was the good kid who always did the right things but got dragged down by Linc all the time.

Lincoln remembered there was one time when Mike was lost. The foster parents had tried everywhere they thought of but still couldn't find Michael. They were worried sick, thinking that some bad things might have happened to him. Michael was just 14 at that time. They decided to search the neighbouring area but Linc insisted to search the nearby streets more closely once again. What made him think that Michael was there was nothing more than the hunch. He just knew.

Back then, it was the hunch that led Linc to the sobbing Michael in the dark alley two blocks away from where they lived. "I miss her," That was all Michael said when he saw Linc. Lincoln put an arm around his little brother, trying his best to comfort him. He knew he could never be as good as their mother. But he swore he would make things right for Michael. He didn't care what he had to give for that.

Nearly 15 years from that time, here they were. He and his son tried to find the missing Michael in Panama City. Despite Linc had made a promise that he would make everything right, he managed to screw everything up. Michael had given up his high-paying job, his loft, his future, his friends, his love and perhaps his soul in his quest of trying to save Lincoln.

Lincoln sighed when he thought of this. "What kind of brother am I?" Lincoln asked himself.

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It started raining again. Linc and LJ didn't even bother to take an umbrella. They walked around the buildings, hoping to catch any sign of Michael.

But there was just nobody on the street.

"Where are you, Michael?" Lincoln sighed again.


	4. Chapter 4

Thank your for your kind support, hollyjonas 101. As a new writer, I could really use some supports from readers. It keeps me motivated! So, feel free to drop any comments!

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**CHAPTER FOUR**

Michael saw Lincoln and LJ when they got out of their car. He felt surprised and at the same time, not surprised. Somehow, he knew LJ was going to tell his dad. He thought of getting away after LJ left. However, how far could he go? He had no car, no food, no clothes, no money, nothing.

He wanted to see Lincoln, the only brother he had in this world. That was why he travelled back here two days ago. But once he arrived, he knew he would do Lincoln more harm than good. "I would destroy everything he has right now," Michael knew this from the bottom of his heart. "And he has a family," he added when he thought of his nephew and Sophia. He just couldn't find Lincoln like nothing ever happened. That was why Michael was here, sitting in one of the dark alleys in the Panama City.

It seemed that everyone was trying to get to him these days. The FBI, the Panamanian police, the Company and now it was Lincoln. Michael felt he had had enough. No matter how hard he tried, there were always strings that pulled him back to where he started. He could never run away.

Feeling desperate, Michael sat down in the dark corner hoping that Lincoln wouldn't see him. He prayed that the ridiculously heavy rain would block Lincoln's vision. Or they would suddenly realize they should simply give up and leave. Sitting down alone, Michael thought about how his life had turned upside down like this. He thought about Fox River, Panama, Sona and … Gretchen. Gretchen, the nasty bitch, was the one Michael wanted nothing but to forget. He hated her because she beheaded the only woman he ever loved – Sara. He felt a stabbing pain through his heart every time he thought of Sara. "Sara," Michael whispered and buried his head in his hands.

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"Michael," someone called. Michael looked up and saw Lincoln right in front of him, with LJ next to him. Michael decided that he was definitely out of luck.

"Michael, are you okay? Are you hurt?" Lincoln said again and began to check whether Michael was hiding any injury.

Michael didn't reply. His mind was processing thousands of possibilities and consequences at the same time.

Lincoln thought he was going to hug Michael ten thousand times when he saw him. Now that he actually did, he couldn't bring himself to do that. He looked at Michael and felt that he didn't quite know the man in front of him. Michael looked different.

LJ sensed that there was something strange about his dad and uncle. He imagined there would be a warm embrace and they would joke about this silly hide-and-seek thing together. But the reality was the otherwise. The brothers looked distant. "Let's get to the car. It's raining heavily," LJ said, trying to break the suffocating silence between the two adults.

Satisfied that Michael apparently had sustained no injury, Lincoln agreed, "Right. We should go to the car. And then we can talk."

"What do we need to talk about?" Michael replied.

"I don't know. Everything."

"I don't have anything to say."

"Michael, come on. At least tell me …," Lincoln stopped right there, suddenly realized that he had probably said something inappropriate.

"What do you want to know, Linc?" Michael asked coldly.

Lincoln was going to say, "You know what I mean, Mike. Did you kill Gretchen?" But he somehow couldn't bring himself to ask that. LJ didn't have to know what Michael wanted to do to Gretchen. And to be honest, Lincoln didn't want to know too. He didn't think Michael would give up avenging Sara's death but he couldn't bring himself to think that his little brother now became a merciless killer. So, he simply said, "I just thought we could go to my place." He studied Michael, looking at his clothes and face. "And you could have a change of clothes, something to eat and rest," he added.

"I don't need that," Michael replied coldly.

Linc was losing his patience even though he knew he shouldn't. He shouted, "You don't need that? You can't see yourself, can you? Your clothes are dirty and wet. You look like you haven't eaten for days and haven't fucking slept in months, Michael!"

He stepped in front of Michael and pulled him up. "Get off me!" Michael refused. He tried to push Lincoln back but he was never his brother's match. He was the brain and Lincoln was the muscle. Lincoln was practically dragging Michael towards to the car whereas Michael was resisting in whatever way he could.

"Linc, I'll hit you if I have to," Michael shouted.

"Yea, try that," Lincoln was not afraid of threat. He was used to it after spending all his teenage years on the street and being in juvy or prison for more times than he could remember.

"What the hell did Lincoln mean? Did he really think that I wouldn't? That's it," Michael thought. He was suddenly furious. He summoned all his energy and hit Lincoln in the face.

That caught Lincoln off-guard because he didn't believe his younger brother would actually do that. Lincoln fell down on the street and swore angrily, "What the fuck, Michael?"

Michael didn't answer. He jumped on Lincoln and decided to give him another smack in the face. If there were any skills that Lincoln could say he was better than Michael, it would be the fighting ones. He knew what Michael wanted to do and got out of the way before Michael could finish his second attack. He grabbed Michael's arms and sent him to the walls.

LJ was the only audience for this fight. He knew his dad was never able to control his temper well, but what about Uncle Mike? LJ could not recall a time when he saw Michael fight like this. What could he do now? He didn't want his dad or uncle to get hurt. "Hey, chill," LJ managed to say. "Don't fight! Let's just talk! Dad! Uncle Mike!"

Predictably, none of the brothers listened to him. Michael got up and pushed Lincoln towards the rubbish bins. The rubbish was thrown all over the place. Lincoln picked up whatever he could find and threw it to Michael.

It was a pillow case. The feathers inside came out when it was sent off the air. Michael retreated backward as the feathers were blocking his sight. Sensing that it was the right time, Lincoln ran towards Michael and knocked him down using his momentum. He sat on Michael. Michael tried to roll but he couldn't. Lincoln was too heavy for him. Lincoln then hit Michael in the face. Twice.

LJ ran towards his father and grabbed Lincoln's hand when he was planning on his third attack. "Stop, dad!" LJ screamed. "You're hurting him!"

Lincoln stopped. He was breathing heavily. He looked at Michael, who was now lying on the floor trying to catch his breath too. Lincoln stood up finally. Once he got up, he held out his hand for Michael. For a moment, LJ thought his uncle would seize this opportunity and hit his dad. "An eye for an eye," LJ thought.

Michael didn't. Instead, he took Linc's hand and stood up. And from that point onwards, LJ knew that he would never understand the relationship between his dad and uncle. They attacked each other for one moment and then they were absolutely cool about that the next minute. How strange.

"Let's go home," Lincoln announced and began to walk off. Michael, who looked now more tired than he already was, followed Lincoln. LJ was again surprised by Michael's lack of protest but, who cared? He got what he wanted. His father, uncle and him were together at last.

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I've planned that next chapter to be about Michael meeting Sophia. But I never like the Sophia character much so I'm not sure if it's a good direction to take. Anyway, thanks for reading and please leave comments!


	5. Chapter 5

Sorry that it took so long to finally update the story. I was so busy these two weeks. Thanks for your comments too, fatladysing. You're definitely encouraging and make me want to write more! Thanks and I will try my best to write a Lincoln that you and I like 

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**CHAPTER FIVE**

All of them were back to Sophia's house now. The house was small but comfortable. Sophia was a good housewife. She was well-organized and everything one needed could be found in her apartment. It was the place where Lincoln and LJ called home for the past week.

Sophia saw Michael before, back at the exchange point soon after he broke out of Sona. She was too focused on James and she hadn't really had the chance to talk to him. However, she had heard a lot about Michael from Lincoln and LJ. Linc always said that Michael was the smartest person in the world. Sophia had to agree. After all, she never thought anyone could break out of two penitentiaries, not to mention one of them was actually of maximum security. LJ also said that he admired his uncle Mike, who always had a brilliant plan for what he had to do.

However, even though she knew why Michael did all the illegal things in the first place, she somehow still found him scary to be with. When James was still in Sona, he once told her that Scofield was good at manipulating people. James told her not to trust the brothers. She believed him back then. Even it turned out that James was a liar, who was not really as innocent as he claimed, Sophia knew that he did this to protect her. James, a liar or not, always wanted her to be good. So, she found it hard to trust Michael entirely. Perhaps Michael Scofield was not such a good person after all. "Perhaps he lied to Lincoln and LJ too," Sophia thought.

When Sophia opened the door and see Lincoln with Michael, she didn't know how to react. Sophia wasn't astonished that Lincoln could find him. However, she didn't understand why Michael would agree to come to her house. If Michael was such a genius who cared so much about his brother and nephew, why would he show up and endanger their peaceful lives again? Maybe James was right afterall. She had to make Lincoln see the true Michael!

"Hey, Sophia," Lincoln said. "Um… can you make us something to eat?"

Sophia was still looking at Michael, who looked around the house instead of her. "What are you looking at? Figuring how to break out of my apartment?" Sophia wanted to say to Michael but immediately shouted at herself how inappropriate the joke was. Lincoln would definitely be very angry. She needed Lincoln to listen to her, not to get mad at her.

"Sophia," Lincoln called again when Sophia didn't answer him. Sophia took the cue this time and said, "Yes, sure. I'll make something. You boys get a change of clothes first. And um … you make yourself comfortable, Michael." She then entered the kitchen and prepared for the meal.

"Go, LJ. And tidy up. Uncle Mike takes your room tonight," Lincoln told LJ. "No problem," LJ replied and went to his room. He then turned to Michael and said, "Come here, Mike. Let's get changed."

Michael followed Lincoln to his room, where he could see lots of female stuff inside. He never pictured Lincoln as such a man but then people may change. After all Lincoln had been through, he definitely deserved something nice.

"Lincoln, thank you. But I think I should go now," Michael said when Lincoln handed him the dry clothes.

"What are you talking about, man?" Lincoln asked with a question mark on his face.

"I should leave," Michael told Linc the same thing again.

"Why do we have to start this again?" Lincoln said, clearly annoyed that Michael brought up what they argued earlier.

"Because we haven't finished," Michael replied.

"Okay. Good. I want you to stay with me, Michael."

"Linc, that's not what I want," Michael said and continued, "You have Sophia and LJ to take care of now."

"I know. And you stay with us too. We are family," Lincoln said and put his hands on Michael's shoulders. Michael was lost for words suddenly.

"The familial obligation. Wasn't it why I set out to save my brother?" Michael thought. Lincoln now had his name cleared. And he had LJ with him and a good girlfriend. He could start over. That was what Michael intended to do when he planned about breaking him out of Fox River. He did it. He saved Lincoln. They sacrificed a lot in order to get there.

Everything was so perfect for Lincoln now and Michael wouldn't want to destroy it. If Lincoln was sent back to prison, all that had been lost would be for nothing. He wouldn't let that happen.

"I am … I am a wanted man, Lincoln. You know what that means?" Michael looked at Lincoln in the eyes. He needed Lincoln to understand the dangerous game he was playing. He needed to remind Lincoln what mess he was dragging himself into, how he was one step from destroying his perfect life. Michael Scofield – a fugitive in both the United States and Panama – was now in his house. The only right thing that Lincoln should do was to actually kick him out of the house and report to the authority.

Lincoln hesitated when Michael laid out the truth. And Michael saw it. He didn't blame Linc. All sensible people would do the exact same thing. Pull out before it drags you down. It's just common sense.

"Good-bye, Lincoln" Michael said and headed to the door.

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